7DU8

Crystal structure of human Proto-oncogene tyrosine-protein kinase receptor Ret in complex with Selpercatinib

• PDB DOI: https://doi.org/10.2210/pdb7DU8/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2021-01-08 Released: 2022-02-02 
• Deposition Author(s): Miyazaki, I., Ishida, K., Suzuki, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.277 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Literature

Selective RET inhibitor TAS0953/HM06

Miyazaki, I., Ishida, K., Suzuki, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.47 kDa 
• Atom Count: 4,715 
• Modelled Residue Count: 565 
• Deposited Residue Count: 628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase receptor Ret	A, B	314	Homo sapiens	Mutation(s): 0  Gene Names: RET, CDHF12, CDHR16, PTC, RET51 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07949 (Homo sapiens) Explore P07949  Go to UniProtKB:  P07949
PHAROS:  P07949 GTEx:  ENSG00000165731

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q6G (Subject of Investigation/LOI)	C [auth A], D [auth B]	Selpercatinib C29 H31 N7 O3 XIIOFHFUYBLOLW-ZRZAMGCNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.277 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.771	α = 90
b = 80.265	β = 99.61
c = 79.91	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): Miyazaki, I., Ishida, K., Suzuki, T.

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection